Hi @xyaous ,
The short answer is that I don’t know, however you are not the first person to notice this happening in one of our data sets for a gene (e.g., this post: Known protein not detected by RNA explorer).
I think any of your suggestions are reasonable. In some cases the differences are technical, although it seems unlikely here since at least three human and one mouse data sets show similarly low expression of CHRM4 across most cells–so also not likely a cross-species difference. Another possibility (which I don’t think is likely given how transcripts are selected) is that the reads for CHRM4 might not be properly aligned with the location of the gene annotation in the genome. We can see in both MTG and M1 that reads pile up in both exonic and intronic locations.
What we can safely say is that CHRM4 does not have high expression in very many nuclei collected from human brains across a variety of studies. Finally, while it is possible that CHRM4 is expressed more highly in single cells rather than single nuclei, this does not appear to be the case in mouse (Single-nucleus and single-cell transcriptomes compared in matched cortical cell types).
I’m not sure what possibilities this leaves (maybe previous studies were mistaken?), but hopefully this post at least provides some directions to pursue and rules out some options.
Best,
Jeremy